[Bioperl-l] progress on Bio::Search::Tiling
Mark A. Jensen
maj at fortinbras.us
Wed May 27 18:51:35 EDT 2009
Hi Sendu- thanks--
After I get some more tests together (and they pass), my plan is to move it over
to core, barring any objections. I'll put up a HOWTO with some discussion and
compare/contrast, per your suggestion.
----- Original Message -----
From: "Sendu Bala" <bix at sendu.me.uk>
To: "Mark A. Jensen" <maj at fortinbras.us>
Cc: "BioPerl List" <bioperl-l at lists.open-bio.org>
Sent: Wednesday, May 27, 2009 5:46 PM
Subject: Re: [Bioperl-l] progress on Bio::Search::Tiling
> Mark A. Jensen wrote:
>> With the current bioperl-dev revision of MapTiling (r15712), I get
>> 6/1095 "failures", which you may judge below. The results indicate to
>> me that the algorithm is working, and that the translated dna
>> coordinate transformations (which kick in based on study of the
>> algorithm name) are correct, at least in this limited set.
>> Comments *highly* appreciated-- many thanks for any time you spend
>> considering this.
>> not ok 389 - tricky.wublast(1)
>> # Failed test 'tricky.wublast(1)'
>> # at blast-MapTiling.t line 571.
>> # '0.222'
>> # >
>> # '0.9'
>> # Not sure why frac_identical should be > 0.9, when no reported 'Identities'
>> value is greater than 24% /maj
> That's almost certainly my mistake. For those two cmp tests I just didn't know
> what the answer was supposed to be, so probably picked a figure out of thin
> air based on the subsequent 2 answers.
> You should manually (or by some other independent method) check what the
> correct answers are for those two cmp tests and change them to 'is' tests.
> Thanks for your work on this. I'd be interested in seeing a summary of what
> you've achieved at the end. Especially if you point out areas where the old
> system was getting things wrong - people may want to recheck their results
> with the new modules.
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